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- PDB-8zg9: Y-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin... -

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Basic information

Entry
Database: PDB / ID: 8zg9
TitleY-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase PRT1
ComponentsY-degron,E3 ubiquitin-protein ligase PRT1
KeywordsLIGASE / complex / ZZ-domain / Arabidopsis thaliana / PRT1 / E3-ubiquitin ligase
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the N-end rule pathway / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PRT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.673 Å
AuthorsYang, W.S. / Song, H.K.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A2C3008285 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4030068 Korea, Republic Of
National Research Foundation (NRF, Korea)2022M3A9G8082638 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin.
Authors: Yang, W.S. / Kim, S.H. / Kim, M. / Shin, H. / Lee, J. / Sandmann, A. / Park, O.K. / Dissmeyer, N. / Song, H.K.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Y-degron,E3 ubiquitin-protein ligase PRT1
B: Y-degron,E3 ubiquitin-protein ligase PRT1
C: Y-degron,E3 ubiquitin-protein ligase PRT1
D: Y-degron,E3 ubiquitin-protein ligase PRT1
E: Y-degron,E3 ubiquitin-protein ligase PRT1
F: Y-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,98620
Polymers47,1536
Non-polymers83414
Water4,306239
1
A: Y-degron,E3 ubiquitin-protein ligase PRT1
B: Y-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0288
Polymers15,7182
Non-polymers3106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Y-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules

C: Y-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9796
Polymers15,7182
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
3
D: Y-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules

F: Y-degron,E3 ubiquitin-protein ligase PRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9796
Polymers15,7182
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)48.254, 85.737, 85.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 298 through 324 or resid 326...
d_2ens_1(chain "B" and (resid 298 through 324 or resid 326...
d_3ens_1(chain "C" and (resid 298 through 324 or resid 326...
d_4ens_1(chain "D" and (resid 298 through 324 or resid 326...
d_5ens_1(chain "E" and (resid 298 through 324 or resid 326...
d_6ens_1(chain "F" and (resid 298 through 324 or resid 326...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11TYRTYRTYRTYRAA298 - 3241 - 27
d_12CYSCYSCYSCYSAA326 - 32929 - 32
d_13GLUGLUGLUGLUAA33134
d_14ILEILEPROPROAA333 - 34536 - 48
d_15GLYGLYGLYGLYAA35053
d_16PHEPHEGLNGLNAA352 - 35455 - 57
d_17HISHISPROPROAA356 - 35859 - 61
d_18HISHISHISHISAA36063
d_19LEULEULEULEUAA36265
d_110LEULEUALAALAAA364 - 36567 - 68
d_21TYRTYRTYRTYRBB298 - 3241 - 27
d_22CYSCYSCYSCYSBB326 - 32929 - 32
d_23GLUGLUGLUGLUBB33134
d_24ILEILEPROPROBB333 - 34536 - 48
d_25GLYGLYGLYGLYBB35053
d_26PHEPHEGLNGLNBB352 - 35455 - 57
d_27HISHISPROPROBB356 - 35859 - 61
d_28HISHISHISHISBB36063
d_29LEULEULEULEUBB36265
d_210LEULEUALAALABB364 - 36567 - 68
d_31TYRTYRTYRTYRCC298 - 3241 - 27
d_32CYSCYSCYSCYSCC326 - 32929 - 32
d_33GLUGLUGLUGLUCC33134
d_34ILEILEPROPROCC333 - 34536 - 48
d_35GLYGLYGLYGLYCC35053
d_36PHEPHEGLNGLNCC352 - 35455 - 57
d_37HISHISPROPROCC356 - 35859 - 61
d_38HISHISHISHISCC36063
d_39LEULEULEULEUCC36265
d_310LEULEUALAALACC364 - 36567 - 68
d_41TYRTYRTYRTYRDD298 - 3241 - 27
d_42CYSCYSCYSCYSDD326 - 32929 - 32
d_43GLUGLUGLUGLUDD33134
d_44ILEILEPROPRODD333 - 34536 - 48
d_45GLYGLYGLYGLYDD35053
d_46PHEPHEGLNGLNDD352 - 35455 - 57
d_47HISHISPROPRODD356 - 35859 - 61
d_48HISHISHISHISDD36063
d_49LEULEULEULEUDD36265
d_410LEULEUALAALADD364 - 36567 - 68
d_51TYRTYRTYRTYREE298 - 3241 - 27
d_52CYSCYSCYSCYSEE326 - 32929 - 32
d_53GLUGLUGLUGLUEE33134
d_54ILEILEPROPROEE333 - 34536 - 48
d_55GLYGLYGLYGLYEE35053
d_56PHEPHEGLNGLNEE352 - 35455 - 57
d_57HISHISPROPROEE356 - 35859 - 61
d_58HISHISHISHISEE36063
d_59LEULEULEULEUEE36265
d_510LEULEUALAALAEE364 - 36567 - 68
d_61TYRTYRTYRTYRFF298 - 3241 - 27
d_62CYSCYSCYSCYSFF326 - 32929 - 32
d_63GLUGLUGLUGLUFF33134
d_64ILEILEPROPROFF333 - 34536 - 48
d_65GLYGLYGLYGLYFF35053
d_66PHEPHEGLNGLNFF352 - 35455 - 57
d_67HISHISPROPROFF356 - 35859 - 61
d_68HISHISHISHISFF36063
d_69LEULEULEULEUFF36265
d_610LEULEUALAALAFF364 - 36567 - 68

NCS oper:
IDCodeMatrixVector
1given(0.0308943298057, 0.758527215582, 0.650908598504), (0.75687158655, -0.443094209115, 0.480429935913), (0.652833012231, 0.477811662761, -0.587796795731)-29.9409142478, 30.0816008363, 12.4665006599
2given(-0.354386634375, -0.480553322587, 0.802171189664), (0.56427950826, -0.793951578147, -0.226339409109), (0.745653237058, 0.372437103023, 0.552532220198)-10.113629924, 18.4754563944, -13.7367137947
3given(0.0131958686234, -0.838057173162, -0.545422811737), (-0.338789805845, 0.509459242973, -0.790994783299), (0.940769544845, 0.195221551734, -0.277202469743)5.3437371919, 37.7258697414, 12.0624832195
4given(-0.262793515676, -0.433077883192, 0.862196680119), (0.803104061782, -0.593449615963, -0.0533049647172), (0.534755489984, 0.678425456777, 0.503761318015)-14.4614519683, 21.2596064635, 22.3720618031
5given(0.951948315934, 0.0907923226505, 0.29249129549), (-0.031733840587, -0.920663516817, 0.389065100161), (0.30461018885, -0.379651739032, -0.873542895283)-32.0754408861, 14.3892088778, 51.4675299259

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Components

#1: Protein
Y-degron,E3 ubiquitin-protein ligase PRT1 / Proteolysis 1 protein / RING-type E3 ubiquitin transferase PRT1


Mass: 7858.824 Da / Num. of mol.: 6 / Fragment: ZZ-domain
Source method: isolated from a genetically manipulated source
Details: YKFG / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PRT1, At3g24800, K7P8.9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8LBL5, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Divalents Buffer System 2 pH 7.5 Precipitant Mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.673→42.98 Å / Num. obs: 41405 / % possible obs: 99.03 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.14 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 20.1
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 1.147 / Num. unique obs: 3911 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ZG8

8zg8


Resolution: 1.673→42.98 Å / SU ML: 0.2572 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 3754 4.81 %
Rwork0.2108 74366 -
obs0.212 41346 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.673→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 14 239 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693283
X-RAY DIFFRACTIONf_angle_d0.9954410
X-RAY DIFFRACTIONf_chiral_restr0.0532422
X-RAY DIFFRACTIONf_plane_restr0.006594
X-RAY DIFFRACTIONf_dihedral_angle_d26.36871226
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.715483456717
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.84333076296
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.782882941198
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.617513676919
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS1.05070974215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.673-1.7330.3781150.34272397X-RAY DIFFRACTION94.79
1.69-1.720.36281380.33562795X-RAY DIFFRACTION98
1.72-1.740.35961260.33212702X-RAY DIFFRACTION97.69
1.74-1.760.35531390.33312774X-RAY DIFFRACTION97.98
1.77-1.790.31431440.29922779X-RAY DIFFRACTION97.08
1.79-1.820.30971450.27952719X-RAY DIFFRACTION99.07
1.82-1.850.28051400.27012812X-RAY DIFFRACTION99.39
1.85-1.880.28871430.26162710X-RAY DIFFRACTION99.37
1.88-1.920.26831400.26062806X-RAY DIFFRACTION99.26
1.92-1.950.29141390.25722791X-RAY DIFFRACTION98.99
1.95-1.990.29691490.25612727X-RAY DIFFRACTION98.36
1.99-2.040.32731420.25382766X-RAY DIFFRACTION98.58
2.04-2.080.23511290.23762769X-RAY DIFFRACTION97.87
2.08-2.130.31271440.22252772X-RAY DIFFRACTION99.15
2.13-2.190.2691460.22262816X-RAY DIFFRACTION99.4
2.19-2.260.2261440.21932748X-RAY DIFFRACTION99.45
2.26-2.330.22531420.2252775X-RAY DIFFRACTION99.08
2.33-2.410.27711390.22942796X-RAY DIFFRACTION99.02
2.41-2.510.22421440.21372746X-RAY DIFFRACTION98.67
2.51-2.620.22321390.21572713X-RAY DIFFRACTION97.4
2.62-2.760.221380.20972812X-RAY DIFFRACTION99.86
2.76-2.940.2471340.20082793X-RAY DIFFRACTION99.73
2.94-3.160.21421440.19762809X-RAY DIFFRACTION99.26
3.16-3.480.21211410.18392735X-RAY DIFFRACTION98.49
3.48-3.980.20511330.17252744X-RAY DIFFRACTION97.53
3.98-5.020.15411310.15482802X-RAY DIFFRACTION99.63
5.02-42.980.23271460.1882758X-RAY DIFFRACTION98.27

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